Spanki in pipelines

[…] format. fragments per kilobase of transcript per million (fpkm) values were calculated using cufflinks version v2.0.2 []. for analyses of mouse genes, transcript splice forms were identified using spanki version 0.4.0 []. genes were annotated and gene counts generated using the intersectbed application from bedtools version 2.18.2 []. reads per kilobase of transcript per million (rpkm) values […]

[…] as discussed in müller et al. ()., a set of simulation studies is used to benchmark the proposed methodology by using synthetic rna‐seq reads from the drosophila melanogaster transcriptome. the spanki software (sturgill et al., ) is used for this. in addition to the simulated data study we also perform a comparison for two real data sets: a low and high coverage sequencing experiment using […]

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[…] as discussed in müller et al. ()., a set of simulation studies is used to benchmark the proposed methodology by using synthetic rna‐seq reads from the drosophila melanogaster transcriptome. the spanki software (sturgill et al., ) is used for this. in addition to the simulated data study we also perform a comparison for two real data sets: a low and high coverage sequencing experiment using […]

[…] between the two methods (). complete gene-level output from each program is provided in ., splicing was analysed by multiple complementary approaches. we used the splicing analysis toolkit (spanki) v.0.4.3 (ref. ) to quantify splice junction coverage from alignment files, and to quantify proportion spliced in for splicing events. the astalavista tool was used to characterize events […]

[…] was used to account for the random hexamer-based bias. for the results presented in this study, we used fpkm >1 as a cutoff for gene expression []., we analyzed sex-specific splicing events using spanki 0.4.0 (splicing analysis kit) []. we used the quickjunc utility within spanki, with alignment files generated by tophat as input, to quantify splice junction coverage, requiring an anchor size […]

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